Locus 7564

Sequence ID	3R_DroMel_CAF1
Location	20,279,475 – 20,279,573
Length	98
Max. P	0.965643

overview

Window 3

Location	20,279,475 – 20,279,573
Length	98
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	82.03
Mean single sequence MFE	-22.40
Consensus MFE	-11.46
Energy contribution	-11.66
Covariance contribution	0.20
Combinations/Pair	1.21
Mean z-score	-3.05
Structure conservation index	0.51
SVM decision value	1.58
SVM RNA-class probability	0.965643
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20279475 98 + 27905053
AAAU----GGCUGGUAGCAGGGAGUUGCAAGUGAAAAUGGAAAUGGAAUGAAAAGCU---------UGCAACUCUUAAUGAGUGCGCUGACAUAAAAAUAAUUAUGAAUUA
....----(((..(((.((.((((((((((((....((.........)).....)))---------)))))))))...))..))))))..(((((......)))))..... ( -22.80)
>DroSec_CAF1 88711 98 + 1
AAAU----GGCUGGCAGCAGGGAGUUGCAAGUGAAAAUGGAAAUGGAAUGAAAAGCU---------AGCAACUCUUAAUGAGUGCGCUGACAUAAAAAUAAUUAUGAAUUA
....----(((..(((.((.((((((((.(((....((.........)).....)))---------.))))))))...))..))))))..(((((......)))))..... ( -20.70)
>DroSim_CAF1 96974 98 + 1
AAAU----GGCUGGCAGCAGGGAGUUGCAAGUGAAAAUGGAAAUGGAAUGAAAAGCU---------UGCAACUCUUAAUGAGUGCGCUGACAUAAAAAUAAUUAUGAAUUA
....----(((..(((.((.((((((((((((....((.........)).....)))---------)))))))))...))..))))))..(((((......)))))..... ( -24.80)
>DroEre_CAF1 91483 102 + 1
UGAUGAGGAGCAGGCAGCUGGGAGUUGGAAGUGAAAAUGGAAAUGGAAUGAAAAGCU---------UGCAACUCCUAAUGAGUGCGCUGACAUAAAAAUAAUUAUGAAUUA
......((.(((..((..(((((((((.((((....((.........)).....)))---------).))))))))).))..))).))..(((((......)))))..... ( -26.70)
>DroWil_CAF1 97381 105 + 1
AAAG---GACCAUGGUCCUGGUAAAACAAAAUGAAAAUAAAAAUGCAAAGUAAC---GGCAACAACUGAAACUCUUAAUGAGUGCGCUGACAUAAAAAUAAUUAUGAAUUA
..((---(((....)))))..................................(---(((..(....)..((((.....))))..)))).(((((......)))))..... ( -17.00)
>consensus
AAAU____GGCUGGCAGCAGGGAGUUGCAAGUGAAAAUGGAAAUGGAAUGAAAAGCU_________UGCAACUCUUAAUGAGUGCGCUGACAUAAAAAUAAUUAUGAAUUA
........(((..(((((.....))))).......................................(((.(((.....)))))))))..(((((......)))))..... (-11.46 = -11.66 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	20,279,475 – 20,279,573
Length	98
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	82.03
Mean single sequence MFE	-15.15
Consensus MFE	-7.32
Energy contribution	-7.52
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.48
SVM decision value	-0.02
SVM RNA-class probability	0.525635
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20279475 98 - 27905053
UAAUUCAUAAUUAUUUUUAUGUCAGCGCACUCAUUAAGAGUUGCA---------AGCUUUUCAUUCCAUUUCCAUUUUCACUUGCAACUCCCUGCUACCAGCC----AUUU
.....(((((......)))))...((...........((((((((---------((........................))))))))))..........)).----.... ( -15.36)
>DroSec_CAF1 88711 98 - 1
UAAUUCAUAAUUAUUUUUAUGUCAGCGCACUCAUUAAGAGUUGCU---------AGCUUUUCAUUCCAUUUCCAUUUUCACUUGCAACUCCCUGCUGCCAGCC----AUUU
.....(((((......))))).(((((..........(((((((.---------((........................)).)))))))..)))))......----.... ( -12.66)
>DroSim_CAF1 96974 98 - 1
UAAUUCAUAAUUAUUUUUAUGUCAGCGCACUCAUUAAGAGUUGCA---------AGCUUUUCAUUCCAUUUCCAUUUUCACUUGCAACUCCCUGCUGCCAGCC----AUUU
.....(((((......))))).(((((..........((((((((---------((........................))))))))))..)))))......----.... ( -16.76)
>DroEre_CAF1 91483 102 - 1
UAAUUCAUAAUUAUUUUUAUGUCAGCGCACUCAUUAGGAGUUGCA---------AGCUUUUCAUUCCAUUUCCAUUUUCACUUCCAACUCCCAGCUGCCUGCUCCUCAUCA
.....(((((......))))).(((.(((((.....(((((((.(---------((........................))).))))))).)).)))))).......... ( -15.86)
>DroWil_CAF1 97381 105 - 1
UAAUUCAUAAUUAUUUUUAUGUCAGCGCACUCAUUAAGAGUUUCAGUUGUUGCC---GUUACUUUGCAUUUUUAUUUUCAUUUUGUUUUACCAGGACCAUGGUC---CUUU
.....(((((......))))).((((..((((.....))))....)))).(((.---........)))........................(((((....)))---)).. ( -15.10)
>consensus
UAAUUCAUAAUUAUUUUUAUGUCAGCGCACUCAUUAAGAGUUGCA_________AGCUUUUCAUUCCAUUUCCAUUUUCACUUGCAACUCCCUGCUGCCAGCC____AUUU
.....(((((......)))))...(((.((((.....)))))))................................................................... ( -7.32 =  -7.52 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:04 2006